Research workbench
Crystal structure analysis of a ternary S-domain complex of human signal recognition particle
Analyse Crystal structure analysis of a ternary S-domain complex of human signal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MFQ
- Type
- protein + RNA
- Length
- 343 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 7S RNA of human srp; Signal recognition particle 19KDA protein; Signal recognition…
- UniProt
- P09132, P61011
- Ligands
- MG, CL
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 7S RNA of human srp | rna | 128 | — | — |
| B | Signal recognition particle 19KDA protein | protein | 107 | 30% helix, 16% strand | P09132 |
| C | Signal recognition particle 54KDA protein | protein | 108 | 64% helix, 0% strand | P61011 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.77 | 0.79 | 84 | MG, CL |
| 2 | 923 | 0.67 | 0.74 | 45 | MG |
| 3 | 181 | 0.50 | 0.77 | 21 | empty |
| 4 | 101 | 0.42 | 0.78 | 12 | empty |
| 5 | 113 | 0.34 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 972 Ų buried · 43 hydrogen bonds · protein-nucleic
- A–C · 564 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–C · 139 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1MFQ · Crystal Structure Analysis of a Ternary S-Domain Complex of Human Signal Recognition… · the same entry in another collection · chain A against A, TM-score 1.00
- P09132 · AlphaFold monomer V2.0 prediction for signal recognition particle 19 kda protein (P09132) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P61011 · AlphaFold monomer V2.0 prediction for signal recognition particle 54 kda protein (P61011) · a predicted model of the same protein · chain C against A, TM-score 0.67
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P09132
- Every structure of UniProt P61011
- Elsewhere: RCSB PDB 1MFQ · PDBe 1MFQ · UniProt P09132 · UniProt P61011
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